bids2cite

Create a citation file for a BIDS dataset.

Can also be used to update references, authors and add license to a dataset.

Installation

git clone https://github.com/Remi-Gau/bids2cite.git
cd bids2cite
pip install .

For developers

pip install .[dev]

Basic tests can be run with:

make test
make test-cli

Usage

The most basic usage is:

bids2cite path_to_bids_dataset

An example of call with all the options:

bids2cite "tests/bids" \
    --keywords "foo, bar, me" \
    --description "this is the description of my dataset" \
    --authors_file "inputs/authors.tsv" \
    --skip-prompt false \
    --verbosity INFO

--keywords and --description allow you to pass keywords and description to add to the citation file.

--skip-prompt is set to false (default) to prompt you for information to add to the citation file.

--authors_file points to a TSV file containing potential authors to add citation file. This can be useful if you need to have a single file to keep track of several lab members and only pick the relevant ones to add to a given dataset.

This TSV file must at least have first_name and last_name columns, but can also include ORCID and affiliation columns.

There is a sample TSV in the inputs folder.

Type the following for more info on how to run it:

bids2cite --help